Blog archive (2010–2018) · no longer updatedO'Connor Memory Judgements Lab blog
From 2010 to 2018 I kept a blog about running a memory research lab: fMRI and SPM fixes, coding experiments, academic careers, publishing and open access, and déjà vu. This is the full archive, every post as it was published, with readers' comments.
108 posts · 46,660 words · 294 comments
2010
- Welcome to my research blog
I am a postdoctoral cognitive neuroscientist / experimental psychologist working in the Psychology department at Washington University in St. Louis. I have been here close to two years and my training has involved learning an awful…
- Got it covered
This week, as well as being published in the Journal of Neuroscience (see here ), our article-related artwork was also chosen to go on the cover of the journal. The Journal of Neuroscience - Feb 24,…
- Masking in SPM5
Masking is an extremely useful function within SPM. For example, you might want to see whether your parietal cue-related activation is subsumed by, or independent of, the parietal retrieval-success activation that is reliably found in the…
- Saving Powerpoint 2003 slides as high-quality (300dpi) image files
Every now and again, Microsoft Powerpoint or Excel graphs or illustrations turn out just as you want them. In these situations, it's handy to have a way of saving each slide as a high-quality image file.…
- DOI lookup
The APA 6th Edition of the Publication Guide 'recommends' that we include DOI (Digital Object Identifiers) in our reference list. Now first of all, what are DOIs? Well, they're actually pretty nifty. According to the DOI…
- Whole Brain Mask
Whole brain masks are produced by SPM when estimating a model. They're great to look over if you want to check the extent of participant movement (a quick heuristic is to examine whether movement has been…
- Understanding what SPM does to establish significant 'activations'
I recently came across a web-page I should have committed to memory years ago, when I was first starting to get to grips with SPM analysis: Matthew Brett's Introduction to SPM Statistics It's a fantastically straightforward…
- Keeping residuals after SPM estimation
Occasionally, it's nice to look under the bonnet and see what's going on during any automated process that you take for granted. More often than not, I do this when the automaticity has broken down and…
- Not-so-restful resting connectivity fMRI (pt.1)
Last week, during a very interesting Brain, Behavior and Cognition colloquium given by Steve Nelson , Jeff Zacks asked a thought-provoking question. He wanted to know what fMRI connectivity maps would look like if you performed…
- Not-so-restful resting connectivity fMRI (pt.2)
Things I have (re-)learned this week: - Conducting resting connectivity analyses on 60mins worth of 2s TR fMRI data from 19 participants takes time; - It is always a good idea to do a quick literature…
- Analysis Threshold Masking in SPM
By default, SPM masks the images that contribute to an analysis at the Estimation stage. If a voxel is masked out because it fails to exceed an arbitrary analysis threshold (set to a defulat of 0.8…
- Not-so-restful resting connectivity fMRI (pt.3)
This is proving to be a little more interesting that I had imagined. The particularly noteworthy finding is a null finding - it doesn't seem to matter how you do the connectivity analysis, the recovered maps…
- No peeking...
It has been a busy and exciting few weeks, but I'm now ready to get back to business and do some research! By way of re-introducing myself to my own blog (and the blogs of others),…
- Making SPM faster
Here's an interesting wikibooks page detailing how you can make SPM faster. Some of the tweaks involve simply adjusting the spm_defaults.m to utilise the amount of RAM you have installed at the model estimation stage. Others…
- What a Relief!
1 commentfMRI
fMRI studies, which measure blood oxygenation-dependent (BOLD) signal, do report brain activations. It seems obvious, but it's been subject to debate. Why? - well, largely because validations of the technique have tended to involve stimulating neurons…
- Blogs as a primary outlet for data
Blogs have an important role to play in making science accessible and fun. We're used to seeing blogs used to highlight and wax lyrical about interesting findings , disseminate critical scientific thought , and pass judgement…
- Free Software for Academics
Below is a list of tools I find useful or interesting. Caveat: I use Windows XP on my current work machine. Some of the listed tools are available only for Windows, others are geared at bringing…
- Seamless fMRI Stimulus Presentation
One of the most annoying and stressful things that can happen during an fMRI experiment is for system notifications, pop-ups or even the Windows taskbar to suddenly appear on the screen on which you are presenting…
- Strong Inference or: How I Learned to Stop Proving and Love Falsification
We all know about them - those legendary articles that transcend their fields and attain status as 'compulsory annual reading for scientists.' Their ideologies are pure, their arguments are well reasoned and their applications are manifold.…
- A 'nothing to do with work' post
Over the past few months I've seen a few fantastic videos on youtube. Embrace Life - Sussex Road Safety Ad Video on YouTube www.youtube.com/watch?v=h-8PBx7isoM Google Search Stories - Paris Video on YouTube www.youtube.com/watch?v=nnsSUqgkDwU There's also the…
- Noise-masking with noise
I'm fortunate in that I have my own office. If things get noisy, in the lab, I can shut my door. In fact, to avoid the social awkwardness of shutting my door on lab-mates mid conversation…
- File Renaming in Bulk with Ant Renamer
fMRI scans produce an awful lot of data. Depending on whether you're getting you scanner to output 3D or 4D data, you can end up with one file per measurement, or file per scan. If you're…
- The 80% Rule of fMRI Participants
Only 80% of scheduled participants produce datasets where data from all runs is usable. That's the conclusion I have drawn from my limited experience of scanning participants for research here at Washington University. My running totals…
- International Shipping from the USA
2 commentsMoving
In September we will be leaving St. Louis and moving back across the Atlantic to St. Andrews, Scotland. Unlike when we made the move over here in 2008, my new job is contributing towards the cost…
- Twitter and Customer Satisfaction
1 commentTwitter
I have been particularly impressed with the way certain corporation have adopted the use of twitter in ways that are beneficial to their customers and potential customers. Companies I follow that spring to mind include VodafoneUK…
- Experimenting with dropbox
Dropbox is a fantastically versatile piece of software based on seamless integration of user-defined folders with ' the cloud '. Much has been written about how it can be used for general computing, e.g. from Lifehacker…
- Marsbar script: Save spheres as both .img and .mat files
Below (indented) is a straightforward MATLAB/SPM/Marsbar script for generating separate Marsbar ROI and Nifti ROI spheres (user-defined radius) from a set of user-defined MNI coordinates stored in a text file ('spherelist.txt' saved in the same directory…
- A Postdoctoral Journey
Image via Wikipedia In just under one month, I will be leaving Washington University in St. Louis and moving to Scotland to take up a lectureship at the University of St. Andrews. It's another big move…
- The Physical Reality of fMRI Slice Acquisition Order
Typical fMRI brain scans take a 3D images of the head every few seconds. These images are composed of lots of 2D 'slices' (usually axially oriented) stacked on top of one another. This is where the…
- Backing up fMRI data manually
Whilst Windows easily copies lots of data, it struggles when you ask it to copy lots and lots and lots of data. Teracopy is a neat file copying utility that provides peace of mind as you…
- The Comprehensive Spending Review and Me
We arrived in Scotland, as planned, in September and have spent the last month settling in to our new surroundings. My first few weeks as a lecturer have been hectic. I still don't have any computer…
- The ideas game
It's been a while. Settling in to a new job has been terrifying and tiring in equal measure. The seemingly boundless spending of the early weeks has been replaced by an awfully adult awareness that the…
- Summer Internships
In the past few weeks, a couple of students have approached me asking if I would be willing to take them on as a summer intern. I scrabbled around to gather some information on the sort…
- Life-giving PhD students
Image via Wikipedia Last week, for the first time in just under than three years, I visited the Institute of Psychological Sciences at the University of Leeds . On Thursday attended the Greater Yorkshire Memory Meeting…
2011
- Good habits
Having just skimmed the Lifehacker article below, I started thinking about what habits I have started incorporating into my work-day, and what habits I really need to cultivate. Lifehacker's "Why and How I Switched to a…
- The Life of an Elsevier Editorial System Manuscript
164 commentsPublication
A recent submission to the Journal of Memory and Language , an Elsevier journal has made my hyper-aware of how the way a manuscript's progress through the Elsevier Editorial System (EES) is indicated. For future reference,…
- A nothing-to-do-with-work post: Chickens
1 commentTimewaster
Thanks to Jim Duff and the British Hen Welfare Trust , we re-homed some ex-battery hens this weekend. Video on YouTube www.youtube.com/watch?v=bSvTQ_qmJSY Keeping chickens is something talked about when I was growing up in suburban Stanmore.…
- Elsevier's Research Highlights
On my recent submission of a manuscript to the Journal of Memory and Language (an Elsevier journal), I was faced with the unexpected task of having to provide "Research highlights" of the submitted manuscript. Elsevier describe…
- Remote Desktop Improvements
Speed Here's a link to some pretty useful tweaks for getting the most speed possible out of a Windows Remote Desktop connection: The end result isn't too much faster than when using the default settings for…
- SPM: Changing the default number of tabulated local maxima
SPM will, by default, show you 3 local maxima within each cluster displayed when you click 'whole brain' within Results. To change the default number of local maxima displayed in the output table, edit spm_list.m and…
- Despite Steve Jobs' best efforts, I have ordered an iPad
Last night I capitulated and ordered an iPad2. Since blogging about whether it might be a good idea to get one a while ago, I have noticed mention of iPads cropping up more and more in…
- A nothing-to-do-with-work post
Some of my favourite youtube videos of the past couple of weeks: Video on YouTube www.youtube.com/watch?v=C_CDLBTJD4M Video on YouTube www.youtube.com/watch?v=gJ6APKIjFQY Video on YouTube www.youtube.com/watch?v=jU4oA3kkAWU and finally... Video on YouTube www.youtube.com/watch?v=e8VL6wJb9uM
- Grant-writing resources
I have almost emerged from one of the most challenging times in my first year at St Andrews, a period of sustained grant-writing. Below are some tips and resources that have helped me during the past…
- A Personal Take on Public Speaking
4 commentsCareer
Tomorrow I travel to Saarbrucken to give an invited seminar at Saarland University. It will be my seventh and penultimate talk of the academic year (with my last talk scheduled for ICOM in York at the…
- Of Google+, Mechanical Turk and Academic Early-Adopters
Having deleted my facebook account nearly two years ago, as I activated a Google+ account this week I was wary of repeating previous mistakes. Back in 2009 I had decided that I wasn't getting as much…
- The non-breaking space
The non-breaking space looks like a normal space, but prevents an automatic line-break from occurring between the two text items it connects. Wikipedia link: Non-breaking space I use it when I want words not to get…
- Surviving your first academic post
2 commentsCareer
I'm taking part in a Guardian live chat this Friday (1-4pm BST) titled 'Surviving your first academic post.' With this topic in mind, I'm noting some preliminary thoughts under a few themes. The points below relate…
- Reading pdf documents on an iPad
Can the iPad2, with its 132ppi 1024 x 768 screen, be used to comfortably read pdfs without the need to zoom and scroll about single pages? That was a question that troubled me when I was…
- E-mail etiquette: How to make contact with academics
Academics are a diverse bunch. Those in my department of just under 40 lecturers and teaching fellows span an estimated 40-year age-range, at least 10 different nationalities and the full spectrum of technological competence. Some were…
- Another mosaic
The image below is to be used to showcase my research in the department foyer. Click to enlarge It is an adaptation of a panel from a figure in my Journal of Neuroscience paper . The…
- Note to future-self
4 comments
As time passes, I feel a growing unease with what I have previously written. The further I am temporally from the moment of expression, the less connected to it I feel. The more likely I am…
- Call for PhD Applications
2 commentsfMRI
Out with the old, in with the new: Novelty judgements as a translational tool to assess healthy ageing Funding Notes: The student will require a minimum of an upper second class Hons Degree and is open…
- SPM: DICOM Import Error
Since setting up lab in St Andrews I've consistently run into a DICOM Import Error that causes the process to terminate about half-way through. I finally fixed the problem today after a quick search on the…
- Embedding Prezis into Wordpress.com Blogs
Having experimented with prezi a fair amount recently, I've been looking at ways to showcase the output on this blog, hosted on wordpress.com. Pasting the standard embed code into the 'HTML editor' just results in a…
- Internet Tools for Academics
1 commentPrezi
Prezi presentation prezi.com/ovkocojtyccv/ Prezi 'slides' for a talk I'll be giving at the Research Away Day next Wednesday.
2012
- Imagine what you could do with two 24-inch screens
Did you imagine editing four Matlab scripts at the same time? No, nor did I. But I found myself doing it anyway.
- Thinning grant proposal ideas
Image via Wikipedia Clare Rathbone , a memory researcher at Oxford Brookes, recently sent me the following Unsolicited Advice article by Julianne Dalcanton on how to navigate the early stages of writing a grant proposal: Discover…
- Marsbar error in pr_stat_compute
Do not duplicate I ran into the following error when trying to use a script to make Marsbar extract betas Error in pr_stat_compute at 34 Indices too large for contrast structure This problem occurred when I…
- Music to think, read and code to
4 comments
Image via Wikipedia Here are a number of free online sources of music and background noise that are particularly good for high-concentration tasks. SimplyNoise - Pure white, pink and brown noise (noise) Rainymood - Stormscape (noise)…
- Raspberry Pi and the lab of the future
Raspberry Pi schematic from I think the Raspberry Pi is going to be fantastic, for reasons summed up very nicely by David McGloin - the availability of such a cheap and versatile barebones technology will kickstart…
- That forgetting, embellishing, lying machine
Image via Wikipedia I heard Andrew Bird play his new album Break it Yourself at the Barbican on Monday. Having previewed it on NPR's First Listen the previous week, I was familiar with the gist, but…
- Old PC won't turn on?
2 commentsTechnology
Image via Wikipedia Open it up, find the BIOS or CMOS battery , and give it a wipe clean. That often does the trick. If it does, it won't stay fixed for long - you will…
- Déjà vu all over again
déjà vu (Photo credit: steve loya) In what feels like a former life, I did a fair amount of research on déjà vu. In fact, it's the domain in which I cut my psychological teeth, learned…
- Codecademic
Points and badges For the past week or so, I have been working my way through Codecademy's JavaScript tutorials. I can't recommend them highly enough. As things stand, I have a full house of 480 points…
- Converting 3D nifti images to a 4D image with SPM
The past few days have seen my fMRI analysis server taken over by a Linux virtual machine. I have installed FSL , and have been using MELODIC to plough my way through ICA analyses of fcMRI…
- NTDWW
A nothing-to-do-with-work post. Just a couple of soothing videos for a relaxed Friday. Video on Vimeo www.vimeo.com/41009719 Video on Vimeo www.vimeo.com/31158841
- Brain Outlines
Below are some quick-and-dirty brain outline images I'm using in a talk I'm giving in a couple of weeks. I like the calligraphic quality that the axial and sagittal slices have. The coronal image is a…
- Web-based Cognitive Psychology Experiments
This year, I decided to learn how to present cognitive psychology experiments online. Five months in, I'm happy with my progress. Since the second-year of my PhD, when I spent a couple of weeks getting nowhere…
- Modifying DrawFormattedText to allow offset of horizontal centering
To present stimuli for my experiments in the lab, I use Psychophysics Toolbox (Psychtoolbox) in conjunction with Matlab. One limitation of Psychtoolbox is that the included DrawFormattedText function does not allow text to be horizontally centered…
- Exploring Online Experiment Participation with Google Analytics
The lab's first Javascript experiment has been online for about 3 weeks now, and has amassed close to 200 participants. It's been a great experience discovering that the benefits of online testing (60+ participants a week,…
- Moments that take your breath away
I've been enjoying the views from my North Sydney apartment since I moved in. The view is incredible. Image no longer available This morning, a couple of lorikeets landed on my balcony railing. These birds' colours…
- Kookaburras
1 comment
This morning's cackling visitors to the balcony were a pair of kookaburras. Image no longer available Image no longer available The light wasn't great, but the experience of seeing them there, just a few feet away…
- Conference time
1 comment
Tomorrow morning I fly to SfN 2012 in New Orleans. There has been some turbulence in the immediate lead-up to it - an unscheduled flight to Ireland putting back my departure by a couple of days…
- Twitter and Conference Socials
On Monday I gave a talk on how internet tools can be used to make the job of being an academic a little easier . I had given a very short version of the talk to…
- Codecademy Stories
A couple of months ago, the folks at c odecademy were nice enough to respond to a complimentary e-mail I'd sent them by writing something nice back about me and publishing it on their codecademy.com/stories page.…
- My new favourite online tool: IFTTT
IFTTT , if this then that , is an online, multi-service task automation tool I first read about on Lifehacker last year. I finally started using it today, and am seriously impressed. Once you've signed up…
2013
- Twitter on MVPA
I often bang on about how useful twitter is for crowd-sourcing a research community. Today I was reminded of quite brilliant the people on twitter can be at helping to overcome an 'I don't know where…
- Using the Raspberry Pi to Run Cognitive Psychology Experiments
The Raspberry Pi (photo credit: Wikipedia) A few months ago, I suggested that Raspberry Pis could be used as a barebones experiment presentation machine . Since then I have got my hands on one and tinkered…
- Find somewhere to publish with Jane - the Journal/Author Name Estimator
If you're trying to decide on a journal to submit your latest manuscript to, Jane - the Journal/Author Name Estimator , can point you in the right direction. This isn't exactly breaking news, but it's worth…
- Identifying Scientific Misconduct
Finding needle in haystack (Photo credit: Bindaas Madhavi) A former colleague of mine at an institution I no longer work at has admitted to being a science fraudster.* I participated in their experiments, I read their…
- Google Reader dies. I rage.
I am heavily reliant on Google Reader for how I keep up with scientific literature. I have customised RSS feeds for PubMed search terms . I have RSS feeds for journal tables of contents. I access…
- The Life of a Psychological Science Submission
A recent submission to (and rejection from) Psychological Science has provided me with enough information on the editorial process, via Manuscript Central, to blog a follow-up to my Elsevier Editorial System blog of 2011 . (I'm…
- Real world stats: How (not) to win at roulette
14 commentsStats
A group of second-year students asked me to contribute a 'Real World Stats' piece to their new psychology publication, MAZE. I reworked a section from of my most popular statistics lectures on probability theory and roulette.…
- Updated RSS feed
The blog is making a relatively straightforward transition from wordpress.com to a self-hosted wordpress.org installation. As the akiraoconnor.org domain is coming with me there has been very little disruption to Google indexing, which send most traffic…
- Transposing cell references in Excel
The process of rotating data in Excel, such that rows become columns and columns become rows, is pretty straightforward. Copy, and then right-click on the destination and select the 'transpose cells' paste option. Right-clicking to transpose…
- On Open Access
I spent most of this summer in St Andrews writing research papers. This prolonged period of writing gave me time to consider the publication of my own work along lines I haven't fully considered before. I…
- Blogs: Public Engagement for Introverts
Earlier this week, I attended the BBSRC Eastbio Annual Symposium, a meeting for PhD students funded by the BBSRC's doctoral training programme. The theme of this year's meeting was 'Making an Impact'. Alongside one or two…
- Open Access...
pays off in the end. Tweet twitter.com/StAndrewsUniLib/status/375281753692184576
- How much could open access publishers charge?
I'm going to disregard the usual speculation about what type-setter and editorial assistant salaries are, and how much distribution infrastructure costs because these are all tied in to the true costs of publishing from a publisher's…
- Peer Review at Frontiers
3 comments
Frontiers use a pre-publication peer review system that differs from the standard peer-review system used by most traditional journals. After undergoing Independent Review, an initial peer review in which reviewers give star ratings and make comments…
- Fix Prezi Desktop's 'Upload to Prezi.com...' Function
I give all of my lectures and presentations using the cloud-based Prezi . Because of this, I have a subscription, which gives me access to the offline Prezi creator, Prezi Desktop. The major advantage of Prezi…
2014
- Lecturing as a Transferable Skill: The Best Man's Speech
Last weekend I had the honour of being Best Man at a university friend's wedding. It was a beautiful day spent in the sunshine of St Albans and then in the low-ceilinged, close comfort of the…
- Conducting Online Experiments - The How To Guide
This is a guest post from Radka Jersakova ( @RadkaJersakova ), who did her undergraduate degree in my lab and is now working on her PhD at Leeds University and the Université de Bourgogne in Dijon.…
- Required Reviews Completed
- Open Access in Scottish Universities
3 commentsOpen Access
Earlier in the year I was asked by the University of St Andrews Open Access Team to give an interview to a group from the University of Edinburgh Library. I'm certainly no expert, but I'm more…
- Objecting to an Editorial Decision
2 commentsPublication
Last week Ravi Mill and I had a paper accepted to Consciousness and Cognition. It was accepted after 49 weeks with the journal in four rounds of review. The editorial decisions on the paper were: Reject,…
- Publishing in PeerJ
Our latest paper on deja vu has been published in PeerJ today: link here . The publication process was great - a far cry from some of the negative gate-keeping experiences I have had trying to…
2015
- Bad things come in... EIGHTS??
I, like most humans, am bad at understanding randomness and good at spotting patterns that don't necessarily exist . I also frequently have thoughts like: "That's the third time this paper has been rejected. It must…
- @lowpolybot
We had an fMRI paper accepted to the Journal of Cognitive Neuroscience earlier this week. Having got the science out the door, I was able to turn my attention to the fun stuff - a cover…
- Traveling abroad during your PhD
This is a guest post from Radka Jersakova ( @RadkaJersakova ), who did her undergraduate degree in my lab and is now working on her PhD at the University of Leeds. Radka has previously written on…
- Cognitive Neuroscience Journal Publication Costs
1 commentPublication
The Journal of Cognitive Neuroscience have just invoiced me $985 for a paper they agreed to publish earlier this year. This wasn't unexpected - not only did we sign away our copyright, allowing MIT Press to…
- PhD Position Starting September 2016
Come to St Andrews and figure out why déjà vu experiences decrease with age, with me and Ines Jentzsch . FindAPhD Advertisement (full text below) Please email ( [email protected] ) or tweet ( @akiraoc ) me…
2016
- Copying and Verifying Copied Files
Over the past couple of days, I have been archiving published fMRI projects, and copying data from SD cards to start new ones. I have written previously about ways in which I have copied and verified…
- But did you REALLY experience déjà vu?
Is it possible to reliably generate déjà vu in participants? Is it possible to get participants to reliably report déjà vu? These very similar questions are not necessarily as closely linked as we might think. A…
- This is your brain on... déjà vu
At the International Conference on Memory last month, I presented some new work from my lab, a 21 participant, fMRI-scanned, memory experiment. We imaged people's brains as they underwent a procedure that generates sensations likened to…
- Science Communication
A happy consequence of the media exposure I have received is that all sorts of people contact me when they have questions about déjà vu. Often, people want to find out about personal experiences they or…
- Special Issue of Memory on Déjà vu
Call for papers: Déjà vu and other dissociative states in memory A special issue of Memory Submission deadline: 31st July 2017 Guest Editors (email links): Chris Moulin , Akira O’Connor and Christine Wells In recent years,…
2018
- The end
Here's an official announcement that I will no longer be maintaining this blog. 'Official' because the blog hasn't seen an update in a long time. This is just the full stop that ends the sentence. Blogging…